5XLE image
Entry Detail
PDB ID:
5XLE
Keywords:
Title:
Crystal structure of anaerobically purified and anaerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase
Biological Source:
PDB Version:
Deposition Date:
2017-05-10
Release Date:
2018-06-06
Method Details:
Experimental Method:
Resolution:
1.69 Å
R-Value Free:
0.17
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Periplasmic [NiFe] hydrogenase large subunit
Chain IDs:B (auth: L)
Chain Length:552
Number of Molecules:1
Biological Source:Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Polymer Type:polypeptide(L)
Description:Periplasmic [NiFe] hydrogenase small subunit
Chain IDs:A (auth: S)
Chain Length:267
Number of Molecules:1
Biological Source:Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Primary Citation
Ni-elimination from the active site of the standard [NiFe]‐hydrogenase upon oxidation by O2.
J. Inorg. Biochem. 177 435 437 (2017)
PMID: 28967475 DOI: 10.1016/j.jinorgbio.2017.09.011

Abstact

Hydrogenase is a key enzyme for a coming hydrogen energy society, because it has strong catalytic activities on both uptake and production of dihydrogen. We, however, have to overcome the sensitivity against O2 of the enzyme, because hydrogenase is, generally, easily inactivated in the presence of O2. In this study, we have revisited the crystal structures of [NiFe]‑hydrogenase from sulfate-reducing bacterium in the several oxidized and reduced conditions. Our results revealed that the Ni-Fe active site of the enzyme exposed into O2 showed two forms, Form-1 and Form-2. The Ni-Fe active site in Form-1 showed the typical Ni-B (inactive ready) structure, whereas those in Form-2 lost Ni with no relation to an exposure time to O2, and two cysteinyl sulfur ligands made a disulfide bond. On the other hand, the formation of sulfenylation of the cysteinyl ligand to Ni, which is often observed in the oxidized form, did not correlate with the Ni-elimination, but with exposure time to O2.

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